Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012466737.1 CLIM_RS09185 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000020465.1:WP_012466737.1 Length = 430 Score = 239 bits (611), Expect = 9e-68 Identities = 146/423 (34%), Positives = 227/423 (53%), Gaps = 14/423 (3%) Query: 2 NDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQ 61 N + Y F T +H+ +Q S PI+ + ++ ++ A A++F ++ G Y R Sbjct: 3 NLQTPYRFETLQVHAGQQPDPTTKSRAVPIYQTTSYTFDSAAHGADLFALREFGNIYTRL 62 Query: 62 GNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLW 120 NPT E ++ +E GK+ + A+G +A + L + GD +VSS++L+G T N Sbjct: 63 MNPTTDVFEQRVAALEGGKAALAVASGHSAQFIALTSLCQAGDTIVSSSYLYGGTYNQFK 122 Query: 121 MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGIL 180 + G G V VD D A+ T+ +++E+I NP V D + I + E GI Sbjct: 123 VAFGRLGITVKFVDGNDPSAFREAVDDRTKALYLESIGNPAFHVPDFEAIAAVAGEHGIP 182 Query: 181 YVVDNTM-TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW--TRYPHIA 237 VVDNT YL RP GA +VV S TK IGGHG ++GG + D G FDW ++P ++ Sbjct: 183 LVVDNTFGCCGYLCRPLQHGASIVVESATKWIGGHGTSMGGVIVDGGTFDWGNGKFPMLS 242 Query: 238 E--------NYKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECK 289 E +++ + + R + LRDFG + P + + G ET++LR +R Sbjct: 243 EPSEGYHGLKFRETFGDLAFIIKARVEGLRDFGPVISPFNSFMLLQGLETLSLRVQRHAD 302 Query: 290 NALALAQMLQADERVAAVYYPGLESHPQHALS-KALFRSFGSLMSFELKDGI-DCFDYLN 347 N L LA+ L A VA V YPGLE HP H + + L FG +++F +K G + ++ Sbjct: 303 NTLELARWLAAHPSVAWVNYPGLEEHPTHRQALRYLTNGFGCVLTFGIKGGYEETVRFIE 362 Query: 348 RLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADF 407 +RLA +N+GD +TLVI A T ++ E +++ G++ ++RVSVG+E DD+ ADF Sbjct: 363 SVRLASHLANVGDAKTLVIHPASTTHQQLSPEEQSAAGVSLDMVRVSVGIEHIDDIKADF 422 Query: 408 RQA 410 QA Sbjct: 423 EQA 425 Lambda K H 0.319 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 468 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 413 Length of database: 430 Length adjustment: 32 Effective length of query: 381 Effective length of database: 398 Effective search space: 151638 Effective search space used: 151638 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory